BICF ChIPseq is a bioinformatics best-practice analysis pipeline used for ChIP-seq (chromatin immunoprecipitation sequencing) data analysis at [BICF](http://www.utsouthwestern.edu/labs/bioinformatics/) at [UT Southwestern Dept. of Bioinformatics](http://www.utsouthwestern.edu/departments/bioinformatics/).
BICF ChIPseq is a bioinformatics best-practice analysis pipeline used for ChIP-seq (chromatin immunoprecipitation sequencing) data analysis at [BICF](http://www.utsouthwestern.edu/labs/bioinformatics/) at [UT Southwestern Department of Bioinformatics](http://www.utsouthwestern.edu/departments/bioinformatics/).
The pipeline uses [Nextflow](https://www.nextflow.io), a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
9. fastq_read2 name of fastq file 2 for PE data
+ See [HERE](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/blob/master/test_data/design_ENCSR729LGA_PE.txt) for an example design file, paired-end
+ See [HERE](test_data/design_ENCSR729LGA_PE.txt) for an example design file, paired-end
+ See [HERE](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/blob/master/test_data/design_ENCSR238SGC_SE.txt) for an example design file, single-end
+ See [HERE](test_data/design_ENCSR238SGC_SE.txt) for an example design file, single-end
##### 3) Bash Script
+ You will need to create a bash script to run the CHIPseq pipeline on [BioHPC](https://portal.biohpc.swmed.edu/content/)
+ This pipeline has been optimized for the correct partition
+ See [HERE](https://git.biohpc.swmed.edu/bchen4/chipseq_analysis/raw/master/docs/CHIPseq.sh) for an example bash script
+ See [HERE](docs/CHIPseq.sh) for an example bash script
This example worklow is derived from original scripts kindly contributed by the Bioinformatic Core Facility ([BICF](https://www.utsouthwestern.edu/labs/bioinformatics/)), in the [Department of Bioinformatics](https://www.utsouthwestern.edu/departments/bioinformatics/).
## Citation
Please cite individual programs and versions used [HERE](https://git.biohpc.swmed.edu/bchen4/chipseq_analysis/raw/master/docs/references.txt). Also, please look out for our pipeline to be published in the future [HERE](https://zenodo.org/).
Please cite individual programs and versions used [HERE](docs/references.txt). Also, please look out for our pipeline to be published in the future [HERE](https://zenodo.org/).
